Investigate composition of HNA/LNA populations and relate them to the productivity of Muskegon Lake
On Wednesday, April 5th @prubbens ran an analysis without the three outliers. His analysis is in analysis_prod2_remov_outliers.ipynb and pulled out the following 11 OTUs that are associated with heterotrophic productivity:
| OTU | Phylum | Class | Order | Family | Genus | Species |
|---|---|---|---|---|---|---|
| Otu000016 | Proteobacteria | Betaproteobacteria | Burkholderiales | betII | Pnec | PnecB |
| Otu000025 | Bacteroidetes | Cytophagia | Cytophagales | bacIII | bacIII-A | Unclassified |
| Otu000034 | Verrucomicrobia | Opitutae | Opitutae_vadinHA64 | Opitutae_vadinHA64_unclassified | Unclassified | Unclassified |
| Otu000040 | Verrucomicrobia | Verrucomicrobia_unclassified | Verrucomicrobia_unclassified | Verrucomicrobia_unclassified | Verrucomicrobia_unclassified | Unclassified |
| Otu000041 | Verrucomicrobia | [Spartobacteria] | [Chthoniobacterales] | verI-B | Xip-B1 | Unclassified |
| Otu000042 | Planctomycetes | Phycisphaerae | Phycisphaerales | Phycisphaeraceae | CL500-3 | Unclassified |
| Otu000050 | Planctomycetes | Phycisphaerae | Phycisphaerales | Phycisphaeraceae | CL500-3 | Unclassified |
| Otu000067 | Bacteroidetes | Flavobacteriia | Flavobacteriales | bacII | bacII-A | Unclassified |
| Otu000082 | Chlorobi | Chlorobia | Chlorobiales | OPB56 | Unclassified | Unclassified |
| Otu000176 | Proteobacteria | Deltaproteobacteria | Bdellovibrionales | Bacteriovoracaceae | Peredibacter | Unclassified |
| Otu000219 | Proteobacteria | Betaproteobacteria | Burkholderiales | betIII | betIII-A | betIII-A1 |
On Wednesday, April 5th @prubbens ran an analysis without the three outliers and with an additional correlational filtering step. His analysis is in analysis_prod2_corrfiltering.ipynb and pulled out the following 3 OTUs that are associated with heterotrophic productivity:
| OTU | Phylum | Class | Order | Family | Genus | Species |
|---|---|---|---|---|---|---|
| Otu000060 | Proteobacteria | Alphaproteobacteria | Sphingomonadales | alfIV | alfIV_unclassified | Unclassified |
| Otu000357 | Proteobacteria | Betaproteobacteria | Burkholderiales | betI | betI-B | Rhodo |
| Otu000124 | Verrucomicrobia | Opitutae | Opitutales | Opitutaceae | Opitutus | Unclassified |
On March 17th, @prubbens performed a randomized lasso in analysis_prod2.ipynb that pulled out the following 12 OTUs that are associated with heterotrophic productivity:
The taxonomy associated with the above OTUs (from data/Chloroplasts_removed/nochloro_taxonomy.tsv) is:
| OTU | Phylum | Class | Order | Family | Genus | Species |
|---|---|---|---|---|---|---|
| Otu000123 | Proteobacteria | Betaproteobacteria | Burkholderiales | betVII | betVII-B | betVII-B1 |
| Otu000027 | Proteobacteria | Betaproteobacteria | Burkholderiales | betI | betI-B | Rhodo |
| Otu000043 | Proteobacteria | Betaproteobacteria | Burkholderiales | betI | betI-A | Lhab-A2 |
| Otu000057 | Proteobacteria | Betaproteobacteria | Methylophilales | betIV | betIV-A | Unclassified |
| Otu000176 | Proteobacteria | Deltaproteobacteria | Bdellovibrionales | Bacteriovoracaceae | Peredibacter | Unclassified |
| Otu000005 | Cyanobacteria | Cyanobacteria | SubsectionI | FamilyI | Unclassified | Unclassified |
| Otu000048 | Proteobacteria | Alphaproteobacteria | Rhodospirillales | alfVIII | alfVIII_unclassified | Unclassified |
| Otu000040 | Verrucomicrobia | Verrucomicrobia_unclassified | Verrucomicrobia_unclassified | Verrucomicrobia_unclassified | Verrucomicrobia_unclassified | Unclassified |
| Otu000058 | Proteobacteria | Gammaproteobacteria | Methylococcales | gamI | gamI_unclassified | Unclassified |
| Otu000067 | Bacteroidetes | Flavobacteriia | Flavobacteriales | bacII | bacII-A | Unclassified |
| Otu000029 | Bacteroidetes | Cytophagia | Cytophagales | bacIII | bacIII-B | Algor |
| Otu000025 | Bacteroidetes | Cytophagia | Cytophagales | bacIII | bacIII-A | Unclassified |